Chemfp 3.3 is now available to licensed users. If you are interested in purchasing a chemfp license, email me.
This release focused on squeezing out even more performance for machines with the POPCNT and AVX2 instruction sets. I believe chemfp is the fastest available single-threaded similarity search program for chemical fingerprints.
Releative to chemfp 1.5 (the latest free version of chemfp), version 3.3 is about 20-35% faster for 166-bit searches, 20-25% faster for 881-bit searches, and around 50% faster for 1024- and 2048-bit searches.
Relative to chemfp 3.2.1 (the previous version of chemfp), version 3.3 is 60% faster for 166-bit fingerprints, 15% faster for 881-bit fingerprints, 25% faster for 1024-bit fingerprints, and 15% faster for 2048-bit fingerprints.
For more information, see the What's New section of the chemfp 3.3 documentation.